staff

Asier Ullate Agote

Postdoctoral fellow in Artificial & Natural Evolution

  • T: +41 22 379 67 82
  • office 4022a (Sciences III)
  • Impact of genome architecture on the functional activation and repression of Hox regulatory landscapes. BMC Biol. 2019 07;17(1):55. 10.1186/s12915-019-0677-x. 10.1186/s12915-019-0677-x.

    abstract

    The spatial organization of the mammalian genome relies upon the formation of chromatin domains of various scales. At the level of gene regulation in cis, collections of enhancer sequences define large regulatory landscapes that usually match with the presence of topologically associating domains (TADs). These domains often contain ranges of enhancers displaying similar or related tissue specificity, suggesting that in some cases, such domains may act as coherent regulatory units, with a global on or off state. By using the HoxD gene cluster, which specifies the topology of the developing limbs via highly orchestrated regulation of gene expression, as a paradigm, we investigated how the arrangement of regulatory domains determines their activity and function.

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  • A Step-by-step Guide to Assemble a Reptilian Genome Chapter in "Methods in Molecular Biology - Avian and Reptilian Developmental Biology".

    abstract

    This volume discusses recent advances in avian and reptilian biology that have caused this diverse field to re-emerge. The chapters in this book are divided into 4 parts: genomics and transcriptomics, genetic manipulation, stem cells, and new model systems. Part I details how to perform genomic and transcriptomic analyses in birds and reptiles; Part II highlights technological advancements in avian genetic manipulation; Part III focuses on methods to handle pluripotent cells; and part IV looks at the emerging models in avian and reptilian developmental biology. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Cutting-edge and comprehensive, Avian and Reptilian Developmental Biology: Methods and Protocols explores a variety of approaches and different sauropsid models that will help facilitate communication and collaboration among researchers, which in turn will progress this field forward.

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  • The SIB Swiss Institute of Bioinformatics' resources: focus on curated databases. Nucleic Acids Res. 2016 Jan 4;44(D1):D27-37. doi: 10.1093/nar/gkv1310. Epub 2015 Nov 28

    abstract

    The SIB Swiss Institute of Bioinformatics (www.isb-sib.ch) provides world-class bioinformatics databases, software tools, services and training to the international life science community in academia and industry. These solutions allow life scientists to turn the exponentially growing amount of data into knowledge. Here, we provide an overview of SIB's resources and competence areas, with a strong focus on curated databases and SIB's most popular and widely used resources. In particular, SIB's Bioinformatics resource portal ExPASy features over 150 resources, including UniProtKB/Swiss-Prot, ENZYME, PROSITE, neXtProt, STRING, UniCarbKB, SugarBindDB, SwissRegulon, EPD, arrayMap, Bgee, SWISS-MODEL Repository, OMA, OrthoDB and other databases, which are briefly described in this article.

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  • The genome sequence of the corn snake (Pantherophis guttatus), a valuable resource for EvoDevo studies in squamates. Int. J. Dev. Biol. 2014 ;58(10-12):881-8. 150060at. 10.1387/ijdb.150060at.

    abstract

    Squamates (snakes and lizards) exhibit a striking variety of phenotypes, with little known on their generative mechanisms. Studies aiming to understand the genetic basis of this wide diversity in morphology, physiology and ecology will greatly benefit from whole genome sequencing initiatives, as they provide the foundation for comparative analyses and improve our understanding of the evolution, development and diversification of traits. Here, we present the first draft genome of the corn snake Pantherophis guttatus, an oviparous snake that we promote as a particularly appropriate model species for evolutionary developmental studies in squamates. We sequenced 100-base paired-end reads from multiple individuals of a single family (parents and offspring) that produced a genome assembly of 1.53 gigabases (Gb), roughly covering 75% of the expected total genome size, and 297,768 scaffolds >1 Kb. We were able to fully retrieve 86, and partially another 106, of the 248 CEGMA core genes, indicating that a high genome completeness was achieved, even though the assembly is fragmented. Using MAKER2, we annotated 10,917 genes with high confidence (Annotation Edit Distance (AED)<1) and an additional 5,263 predicted genes matched with the species' transcriptome. Numerous colour and colour pattern morphs exist in P. guttatus, making it an ideal model to study the genetic determinism, development, and evolution of adaptive colour traits in reptiles. Using our draft genome and a Single-Nucleotide Polymorphism (SNP) calling approach, we confirmed the interval with the causative mutation for the amelanistic phenotype, a result supported by a parallel exome-based study.

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